The new folder hierarchies are actually created by your application (Outlook or other). This is normal behaviour for all accounts of the IMAP type.

The answer to the question is simple, but disappointing:

You can't have the cake and eat it :-((

Or, on the more serious side:

When you choose for IMAP (bi-directional folder synchronization), your application can only keep track of the changes when it creates and maintains this separate folder hierarchy. Otherwise, it would not know how to distinguish between messages from various sources.

We understand that it may take a bit to get familiar with this behaviour of IMAP mailboxes. Remember that your application does not just download the messages, but creates a shadow copy of the mailbox contents. The 'master copy' of the messages remains on the mail server. [read more...] 

To combine the best of the two worlds (POP3 and IMAP), you may want to try the following:

Define both a POP3 and an IMAP account pointing to the same mailbox. A POP3 download will deliver the messages into the usual Inbox, whereas the IMAP account allows you to take a look at the other folders (including _Junk and _Trash).

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